If you are flying into Narita Airport, as most people from outside of Japan going into Tokyo do, I would highly reccomend buying a JR Rail Pass. It can be used immediately on the Narita Express, which will get you into Tokyo and to Tokyo Station.
The Pass is also helpful if you plan to make day trips to places like Kyoto or Sendai. It is also much faster and much less expensive than taking a taxi from the airport.
A JR Rail pass can be purchased from the following web site Japan Rail Pass. The site offers passes for sale and has 7 different langauge pages to choose from.
This is a popular route to/from Shinjuku and Hakone. You can buy the Hakone Freepass which offers return train ticket on Odakyu Line to/from Shinjuku/Hakone and unlimited rides on its Hakone trains, buses, cable cars and ropeways.
I purchased the Hakone Weekday Freepass at 4700 yen per person. The ticket is valid for 2 days. If you want to travel in luxury, pay an extra 870 yen one-way and sit on the "Romance" car. The trip lasts 1.5 hours and is normally non-stop from Shinjuku to either Odawara or Hakone-yumoto.
1-1-3 Nishi-shinjuku, Shinjuku, Tokyo, 160-8309 Japan
Just a warning if you have a fear of being in tight spaces. DO NOT travel real early morning, if you are going into tokyo. I myself don't have this problem , but got a bit scared . You will get pushed off and on the train at each stop. So just be prepared
Like "All Roads Lead to Rome" - all railroads lead to Tokyo in Japan.
Better know to foreigners as the "bullet trains". These trains can reach average speeds of 280Kmp/h and serve all major cities on the island of Honshu and as far south as Hakata, the train stop which serves Fukuoka. Tokyo is well served by the shinkansen, they pass through en-route to either Osaka / Kyoto and as far south to Hakata or in the opposite direction north reaching Niigata and Akita, going almost every 30 min or so during the day.
The shinkansen is definately the best way to travel in Japan and can be even used by the "budget" traveller, that's being budget minded for Japan! It is important to know that discounted tickets for 7, 14 and 30 days unlimited travel can be bought, but must be purchased outside of Japan. This makes Japan a viable travel option as a short trip of 7 days for example from Korea. A seven days JR (Japan Rail) pass, valid for all JR train travel, including shinkansen, can be purchased at a number of travel agents / ferry booking offices in Korea for about 300,000won (US$260), a real bargin!
Kamakura is the original capital of Japan (currently Tokyo, previously Kyoto). By JR it is approximately 1 hour train ride from Tokyo station. This is perfect mode of travel if you are pinching your dollar (or yen) and not in a hurry. Also great for people watching, you get to meet and see more locals in their day to day life.
Keisei Line from Narita Airport Terminal 1 and 2 to Ueno or Nippori is the cheapest way to Tokyo. You can buy the ticket at Narita both Terminal 1F. An hour from Narita to Ueno Station with only 2000JPY.
Narita Express is one of the most convenient way to reach Tokyo from Narita Airport. The service is regular hourly and on peak hours every half an hour. The journey takes about 53 minutes to Tokyo station. The ordinary seats are very comfortable and leg space is wide. The ordinary one-way ticket costs about 3000 JPY to Tokyo. If you get Suica&NEX card, you will get a huge discount on Narita Express to Tokyo. You can get more details on that in my suica card tip.
The JR and various train lines can initially be quite daunting, but if you spend a bit of time at the station reading up & studying the lines, you'll be fine.
Within metropolitan Tokyo, there are English wordings at all stations. I was able to get all the way from Shinjuku station to Narita town & airport and Disneyland, Chiba (about 2 hours out of Tokyo town) with little difficulty. However, once you get to the outskirts of Tokyo, there might not be as many stations with English wordings.
I found the people manning the Information Counter to be extremely helpful. The ones I met all spoke English and were clear in outlining the various options and they even provided my husband and I with a little mini route map. If you have to choose, approach a lady rather than a man. The ladies tend to smile more and are friendlier. The men tend to be brusque and more impatient.
*Updated (2009): A Useful Tip: "Topping-Up Ticket" Machine*
As for the ticket, if you underpay when you purchase the ticket, you can top up the ticket difference on the other side, so don't worry at all about getting it right. That's why I observed that many people simply purchase the lowest value tickets, and then ride the subway freely. When they get out on the other side, they would top up the difference using the top-up machine.
What the machine does is read the value on your ticket, the station that you had commenced your journey on, and calculate the difference by which you have to top up. This works even when you've changed stations numerous times, within the same train or JR network.
The Tokyo Metropolitan Government has prepared some tips for tourists on how to travel around Tokyo using various transport options - click on the link below
Tokyo is like a maze of Train lines...
It's sometimes hard to find which line to use and where to get off and such only on guide books or signs.
So, I'll introduce to you 2 websites where you can search train routes in English!
This site allows you to search routes within Tokyo and its neighbouring areas only by clicking on your mouse.
You can search routes anywhere in Japan on this site, but you can't use if you misspell the station names.
I have pasted the information from Japan Tourism Board here.
It's cheaper if you are planning to use the train on other days or pay 3000 yen for airport shuttle.
(The Japan Rail Pass is available only to people from abroad who wish to come to Japan as "temporary visitors" for sightseeing. It is usually necessary to purchase an Exchange Order through a travel agency abroad so that the Exchange Order can be exchanged for a Japan Rail Pass after entering Japan.
It is very important to remember that only those who receive the entry status "temporary visitor" stamped in their passports are eligible to obtain the Japan Rail Pass. In order to receive your Japan Rail Pass, you need to take your Exchange Order to an applicable Japan Rail station, upon arrival in Japan, which has a Japan Rail Pass exchange office.
The Exchange Order of Japan Rail Pass can be purchased from overseas offices of JTB Corp., JALPAK, Nippon Travel Agency Co., Ltd., Kintetsu International, and Toptour Corporation plus their affiliated travel agencies in various countries. Overseas offices of Japan Airlines(JAL)* and All Nippon Airways(ANA) also handle the Exchange Order. *When using JAL group flight.)
I just loved the shinkansen trains (bullet trains)! Their punctuality, the way they stop at the stations exactly at door marks painted on the platform. The train staff was incredibly polite: they bow at entering and leaving the car and move very discreetly so as not to disturb anyone. But most importantly, the trains are such a quick way of getting places, especially the Nozomi trains, they are the fastest. From Tokyo to Osaka (550 km) in 2,5 hours. Easy and highly recommended.
We encountered a bunch of extremely mild-mannered Japanese travellers, whose seats we had taken by accident, instead of ours. They stood around in one part of the coach, extremely reluctant to ask us to check if we had the right seat numbers etc. It was probably an hour into the journey when they finally asked and we made an embarassed correction to our seating plan! Typically japanese!
The travel time to Kyoto on the ultra-modern Shinkansen was about 2.5 hours. Compare that with the time our coach took getting us from Kyoto to Tokyo - 8 hrs!
pity it was a night train. I missed seeing the sights whizzing past my window...
If you want to go from Tokyo to someplace by JR and the destination is not shown on the faremap at the station, what should you do?
Buy a fare for the furthest station that the train goes on the line that you need to be on, or the next station for that matter. for eg, if you are travelling from Shinjuku to Utsunomiya, and it doesn't show on the faremap, you buy the ticket to Ueno, and travel as normal and transfer, getting to utsunomiya. When you reach your destination, go to the station counter, give him the ticket, and he will calculate the difference in fare and you'll pay the difference. OR if there is a fare difference machine around, you can use that. slot the ticket in and pay the difference as shown on the screen. a new ticket will pop out and you use that ticket to get past the gates.
With the combination of JR and other subway system, you can actually travel around Tokyo without taking other type of transportation. Yamanote (Loop) line should be the most used JR line for tourist as its simple and doesn't have several types of trains like other JR lines.
To NOTE: Most JR lines have 3 types of trains: 1) normal, 2) express and 3) rapid. Where "normal trains stop at every sations, express trains stop in fewer stations and rapid trains stop at ever fewer stations. So its important to know if you are getting the right type of train cuz not every train stops at every station~
Tickets: Buy an IO card for the value of 1,000, 3,000 or 5,000 and you dont need to purchase ticket everytime you take the JR. And you get to keep the card after the value's used up~
The Website: very useful! u might check how to get from one spot to another, where to get transited.. and also the price!